[gmx-developers] triggering GMX_NB_GENERIC produces wrong interactions
Mark Abraham
Mark.Abraham at anu.edu.au
Tue May 11 08:50:52 CEST 2010
On 11/05/2010 4:35 PM, Igor Leontyev wrote:
> Dear gmx-developers,
> I would like to test non-standard nonbonded interaction which can not be
> implemented simply defining tables.
If the interactions are pairwise, being unable to use tables sounds
wildly unlikely. If you discuss your idea, you may learn about a good
way to do it :-)
> According to posts on gmx-developers
> board, the simplest way to do this is to modify "gmx_nb_generic_kernel"
> subroutine. To make use the routine the environment variable
> GMX_NB_GENERIC should be set up. The energy comparison obtained with "set
> GMX_NB_GENERIC=0" and without, however, produces different energies.
> What can be done?
It's probably immaterial, but setting GMX_NB_GENERIC to 1 is a better idea.
Look further back in the .log file to see what mdrun is reporting about
what nonbonded routines it is using.
Life will probably be easier if you do your development and initial
testing work on a single processor.
You shouldn't be using PME, because it requires a particular form for
the nonbonded interactions... (unless that's the target of your test)
Mark
> The system is equilibrated box of 216 SPC/E water molecules. Initial
> temperature, LJ (SR) and Coul. recip. energy terms are the same, while
> Coulomb (SR) term differs essentially. See bellow output of step 0.
>
> openmpi/mpirun -np2 mdrun -s water216.tpr
> ======================================================
> There are: 648 Atoms
> Charge group distribution at step 0: 112 104
> Grid: 4 x 3 x 3 cells
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 0.00e+00
> Initial temperature: 295.174 K
>
> Started mdrun on node 0 Mon May 10 22:43:13 2010
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 1.73768e+03 -1.04948e+04 -1.13345e+03 -9.89062e+03 1.58418e+03
> Total Energy Temperature Pressure (bar)
> -8.30643e+03 2.94714e+02 -9.93848e+02
>
> ======================================================
>
>
>
> export GMX_NB_GENERIC=0
> openmpi/mpirun -np2 mdrun -s water216.tpr
> ======================================================
> There are: 648 Atoms
> Max number of connections per atom is 2
> Total number of connections is 864
> Max number of graph edges per atom is 2
> Total number of graph edges is 864
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 0.00e+00
> Initial temperature: 295.174 K
>
> Started mdrun on node 0 Mon May 10 22:25:39 2010
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Grid: 3 x 3 x 3 cells
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 1.73768e+03 4.18426e+04 -1.13345e+03 4.24468e+04 1.58623e+03
> Total Energy Temperature Pressure (bar)
> 4.40330e+04 2.95095e+02 2.00676e+05
> ======================================================
>
> Igor
>
>
>
>
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